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comparison varamplicnv-5bafb1c69d03/VarAmpliCNV_Count.xml @ 0:febc6023d37b draft

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author geert-vandeweyer
date Fri, 25 Sep 2020 08:29:36 +0000
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1 <tool id="VarAmpliCNV_Count" name="Count Aligned Amplicons" version="0.1.0" >
2 <requirements>
3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 ##prepare input and indices
7 ln -s '$bam' infile &&
8 #if $bam.is_of_type('bam'):
9 #if str( $bam.metadata.bam_index ) != "None":
10 ln -s '${bam.metadata.bam_index}' infile.bai &&
11 #else:
12 samtools index infile infile.bai &&
13 #end if
14 #elif $bam.is_of_type('cram'):
15 #if str( $bam.metadata.cram_index ) != "None":
16 ln -s '${bam.metadata.cram_index}' infile.crai &&
17 #else:
18 samtools index infile infile.crai &&
19 #end if
20 #end if
21
22 ## Run Counter.
23 parseBAM.py '$bed' 'infile' '$counts' '$unmapped' '$stats'
24
25 ]]></command>
26 <inputs>
27 <param name="bed" type="data" format="BED" optional="false" label="Unique Amplicons (BED)" help="This file is created by the VarAmpliCNV 'Annotate Amplicons' tool." />
28 <param name="bam" type="data" format="bam" optional="false" label="BAM file" help="Sequencing data file" />
29 </inputs>
30 <outputs>
31 <data name="counts" format="tabular" label="VarAmpliCNV on ${on_string}: Counts" />
32 <data name="unmapped" format="bam" label="VarAmpliCNV on ${on_string}: UnMapped Reads" />
33 <data name="stats" format="txt" label="VarAmpliCNV on ${on_string}: Statistics" />
34 </outputs>
35 <help>
36 **VarAmpliCNV : Counting**
37
38 BAM files are parsed for readpairs exactly matching specified amplicons, based on start and end position.
39
40 **Parameters are :**
41
42 * Amplicon Design File (BED) : The de-duplicated amplicon list, generated by "varAmpliCNV Annotate".
43 * Sample Data (BAM) : The sample read data, provided as a single BAM file, or a collection of BAM files.
44
45 **Output files :**
46
47 * Count file (txt): the amplicon-read table.
48 * Unmapped (BAM) : Reads not matching amplicons. This bam file can be used to investigate issues.
49 * Stats (txt): Overview of the matching performance. Use it to investigate issues.
50
51 In case a collection of BAM files is provided, the output files will be grouped in collections as well.
52
53 </help>
54 </tool>